Biomedical Engineering Reference
In-Depth Information
service = 'http://apps.ideaconsult.net:8080/ambit2/';
serviceSPARQL = 'http://apps.ideaconsult.net:8080/ontology/';
stringMat = opentox.listDescriptors(serviceSPARQL);
descriptor = stringMat.get(1, 'algo');
molecules = cdk.createMoleculeList();
molecules.add(
cdk.fromSMILES('CC(=O)C1=CC=C(C=C1)N')
);
molecules.add(
cdk.fromSMILES('C1=CC=C(C(=C1)CC(=O)O)NC2=C(C=CC=C2C1)C1')
);
js.say(
descriptor + ' - ' +
opentox.calculateDescriptor(service, descriptor, molecules)
);
service = 'http://apps.ideaconsult.net:8080/ambit2/';
serviceSPARQL = 'http://apps.ideaconsult.net:8080/ontology/';
stringMat = opentox.listDescriptors(serviceSPARQL);
descriptor = stringMat.get(1, 'algo');
molecules = cdk.createMoleculeList();
molecules.add(
cdk.fromSMILES('CC(=O)C1=CC=C(C=C1)N')
);
molecules.add(
cdk.fromSMILES('C1=CC=C(C(=C1)CC(=O)O)NC2=C(C=CC=C2C1)C1')
);
js.say(
descriptor + ' - ' +
opentox.calculateDescriptor(service, descriptor, molecules)
);
This script combines functionality from the Chemistry Development Kit
plug-in for Bioclipse via the cdk BSL extension with the OpenTox
functionality provided by the opentox extension.
The third basic functionality of the Bioclipse-OpenTox interoperability
we highlight here is the support for accessing protected resources within
the OpenTox network. Despite preferences of the authors, we acknowledge
that not all scientifi c data will be Open Data in the foreseeable future. As
such, authentication and authorization (A&A) are important features of
data access. OpenTox implements both aspects, and provides web
services for A&A, allowing users to log in and out of OpenTox
applications, accompanied by policy-based specifi cation of OpenTox
resource access permissions. Additionally, the same mechanism is used to
restrict access to calculation procedures, allowing exposure of software
with commercial licenses as protected OpenTox resources.
Bioclipse was extended to support the authentication functionality,
allowing OpenTox servers to properly authorize user access to particular
web services and data sets. The OpenTox account information is
registered with Bioclipse's keyring system, centralizing logging in and out
onto remote services, providing the GUI for adding a new OpenTox
account and to log in and out. The corresponding script commands for
the authentication are given in Authentication category in Table 2.1.
Support of authentication is important for industrial environments in
which confi dential data are handled.
With these basics covered, we will now turn to two use cases much
more interesting from a toxicology perspective. For these, we will use the
Tres Cantos Antimalarial Compound Set, TCAMS - a collection of
13 533 compounds of the Tres Cantos Medicines Development Campus
of GlaxoSmithKline deposited in 2010 at the ChEMBL Neglected
Search WWH ::
Custom Search